Well I'm not sure about this but I know if you're evil you eventually get the Cursed Seal, but the people with a Good alignment don't really have anything like that to look forward to from what I know.
I was thinking that perhaps they could have the ability to open their Chakra gates.
It's just an idea and it doesn't necessarily have to deal with alignment, but the Opening of Chakra Gates is a nice thing to think about for the game.
I guess it would pretty much increase your strength a whole lot and after it's over you would lose a certain percentage of hitpoints since it is a technique that damages yourself.
I'm not sure if this idea was already stated by someone else but tell me what you think